Bio:n Volume 1 of the comic series Teenage Mutant Ninja Turtles, Dr. Stockman was a mad scientist with no relation to the comic Oroku Saki, or the Shredder. He developed the Mousers with the help of his computer programmer April O'Neil. Around the time of the Mouser's invention, strange bank robberies were being held, with small tunnels leading into the vaults. When April questioned Stockman, he led April to an underground factory where hundreds of Mousers were being made. Stockman revealed he had been using the Mousers to rob banks, not because of the money (he could use his invention to make millions legally), but because "it was FUN!" April tried to escape through the elevator, but the scientist sent the elevator to sewer level. The Teenage Mutant Ninja Turtles saved her from the Mousers Stockman had sent to kill April. Then they successfully infiltrated Stockman's lab, and managed to stop him. He was taken into custody. Later, he reappeared in Volume 2 of the comics as a major villain who had used technology from DARPA to place his brain in a robot body, making him a cyborg. Stockman tried to get revenge on the TMNT, but his new body was electrocuted and assumed to be destroyed; only the glasses he had retrieved earlier remained.

In Volume 4 of the comics, however, it is revealed that Donatello kept the renmants of Stockman's cyborg body and mind hidden from his brothers for years. It was discovered that Stockman had, in Volume 2, injected April with nanobots in her shoulder during an encounter. These nanobots eventually activated and began to destroy her body; they were destroyed but are suspected to have made her sterile (although whether or not she will remain sterile after their destruction has not been explored). Donatello finally destroyed the renmants of Stockman to avenge April, including his mind; however it is possible that Baxter Stockman's entity still somehow exists and is capable of manipulating electronics and devices.